Ben Nicolet
@bnicolet.bsky.social
Postdoc @ Schumacher lab, immunology, ML, TCR, Amsterdam
Can you boost the protein expression in specific cell types?
That is what we asked in our study published a week ago in @scienceadvances
We used machine learning (AI) to learn the code for protein expression in immune cells.
www.science.org/doi/10.1126/...
That is what we asked in our study published a week ago in @scienceadvances
We used machine learning (AI) to learn the code for protein expression in immune cells.
www.science.org/doi/10.1126/...
Learning the sequence code of protein expression in human immune cells
SONAR informs the design of cell type–specific protein expression in human cells.
www.science.org
August 1, 2025 at 8:40 AM
Can you boost the protein expression in specific cell types?
That is what we asked in our study published a week ago in @scienceadvances
We used machine learning (AI) to learn the code for protein expression in immune cells.
www.science.org/doi/10.1126/...
That is what we asked in our study published a week ago in @scienceadvances
We used machine learning (AI) to learn the code for protein expression in immune cells.
www.science.org/doi/10.1126/...
Reposted by Ben Nicolet
it is finally out! 👇 our #ML pipeline SONAR, which can predict the protein abundance in #immune cells. Using sequence features present in the #RNA. With @bnicolet.bsky.social
Supported by the @erc.europa.eu and@oncodeinstitute.bsky.social
www.science.org/doi/epdf/10....
Supported by the @erc.europa.eu and@oncodeinstitute.bsky.social
www.science.org/doi/epdf/10....
Learning the sequence code of protein expression in human immune cells
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www.science.org
July 23, 2025 at 7:07 PM
it is finally out! 👇 our #ML pipeline SONAR, which can predict the protein abundance in #immune cells. Using sequence features present in the #RNA. With @bnicolet.bsky.social
Supported by the @erc.europa.eu and@oncodeinstitute.bsky.social
www.science.org/doi/epdf/10....
Supported by the @erc.europa.eu and@oncodeinstitute.bsky.social
www.science.org/doi/epdf/10....
Reposted by Ben Nicolet
It's not the models, it's the data!
We show that a substantial proportion of a widely used TCR-pMHC database does not functionally validate, causing underestimation of performance of TCR-pMHC prediction models.
www.biorxiv.org/content/10.1...
We show that a substantial proportion of a widely used TCR-pMHC database does not functionally validate, causing underestimation of performance of TCR-pMHC prediction models.
www.biorxiv.org/content/10.1...
A functionally validated TCR-pMHC database for TCR specificity model development
Accurate prediction of TCR specificity forms a holy grail in immunology and large language models and computational structure predictions provide a path to achieve this. Importantly, current TCR-pMHC ...
www.biorxiv.org
May 2, 2025 at 3:57 PM
It's not the models, it's the data!
We show that a substantial proportion of a widely used TCR-pMHC database does not functionally validate, causing underestimation of performance of TCR-pMHC prediction models.
www.biorxiv.org/content/10.1...
We show that a substantial proportion of a widely used TCR-pMHC database does not functionally validate, causing underestimation of performance of TCR-pMHC prediction models.
www.biorxiv.org/content/10.1...
Getting inspired at the EMBL sustainability event!
April 29, 2025 at 9:00 AM
Getting inspired at the EMBL sustainability event!
Super grateful and happy to be part of MATCHMAKERS team of @cancergrand.bsky.social : bit.ly/4iN1dY9
(And thanks to CGC for the opportunity to talk about my work!)
(And thanks to CGC for the opportunity to talk about my work!)
Tackling one of immunology’s greatest questions
Future Leaders Spotlight: Meet MATCHMAKERS with Benoit Nicolet.
bit.ly
January 5, 2025 at 4:18 PM
Super grateful and happy to be part of MATCHMAKERS team of @cancergrand.bsky.social : bit.ly/4iN1dY9
(And thanks to CGC for the opportunity to talk about my work!)
(And thanks to CGC for the opportunity to talk about my work!)
Super grateful and happy to be part of MATCHMAKERS team of @cancergrand.bsky.social : bit.ly/4iN1dY9
(And thanks to CGC for the oppressed to talk about my work!)
(And thanks to CGC for the oppressed to talk about my work!)
Tackling one of immunology’s greatest questions
Future Leaders Spotlight: Meet MATCHMAKERS with Benoit Nicolet.
bit.ly
January 3, 2025 at 9:39 AM
Super grateful and happy to be part of MATCHMAKERS team of @cancergrand.bsky.social : bit.ly/4iN1dY9
(And thanks to CGC for the oppressed to talk about my work!)
(And thanks to CGC for the oppressed to talk about my work!)
Reposted by Ben Nicolet
New preprint 📣📣
Together with Monika Wolker's lab
@sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification.
www.biorxiv.org/content/10.1...
Together with Monika Wolker's lab
@sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification.
www.biorxiv.org/content/10.1...
Single molecule imaging of transcription dynamics, RNA localization and fate in T cells
T cells are critical effector cells against infections and malignancies. To achieve this, they produce pro-inflammatory cytokines, including IFN-gamma and TNF. Cytokine production is a tightly regulat...
www.biorxiv.org
December 12, 2024 at 3:47 PM
(Repost from EMBO on x) Rethinking #sustainability in #science: read about three projects on consumption and waste of shortlisted candidates for the EMBO Lab Sustainability Award
embo.org/people/rethink…
@CanigovaNikola @bnicolet.bsky.social @SELS_Network
embo.org/people/rethink…
@CanigovaNikola @bnicolet.bsky.social @SELS_Network
December 7, 2024 at 10:19 PM
(Repost from EMBO on x) Rethinking #sustainability in #science: read about three projects on consumption and waste of shortlisted candidates for the EMBO Lab Sustainability Award
embo.org/people/rethink…
@CanigovaNikola @bnicolet.bsky.social @SELS_Network
embo.org/people/rethink…
@CanigovaNikola @bnicolet.bsky.social @SELS_Network
Reposted by Ben Nicolet
Looking forward to attend this great meeting!
Calling all T-cell aficionado's.
Come and join us next year (27-28 May 2025) for the fourth Antwerp T-Cell Receptor conference organised by @pmeysman.bsky.social, @krislaukens.bsky.social and Benson Ogunjimi.
I'll also be there!
www.uantwerpen.be/en/conferenc...
#ImmunoSky
Come and join us next year (27-28 May 2025) for the fourth Antwerp T-Cell Receptor conference organised by @pmeysman.bsky.social, @krislaukens.bsky.social and Benson Ogunjimi.
I'll also be there!
www.uantwerpen.be/en/conferenc...
#ImmunoSky
November 22, 2024 at 9:30 PM
Looking forward to attend this great meeting!
Reposted by Ben Nicolet
New preprint 📣📣
Together with Monika Wolker's lab
@sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification.
www.biorxiv.org/content/10.1...
Together with Monika Wolker's lab
@sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification.
www.biorxiv.org/content/10.1...
Single molecule imaging of transcription dynamics, RNA localization and fate in T cells
T cells are critical effector cells against infections and malignancies. To achieve this, they produce pro-inflammatory cytokines, including IFN-gamma and TNF. Cytokine production is a tightly regulat...
www.biorxiv.org
November 12, 2024 at 1:24 PM
New preprint 📣📣
Together with Monika Wolker's lab
@sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification.
www.biorxiv.org/content/10.1...
Together with Monika Wolker's lab
@sanquin Amsterdam, we optimized a smFISH protocol for T cells. We measured cytokines IFNG/TNF expression and localization during T cell activation and optimized an imaging pipeline for quantification.
www.biorxiv.org/content/10.1...
Reposted by Ben Nicolet
Wonderful to see the #immunology community growing here.
The first starter pack is full (they cap at 150), so I created a second one. Let me know if you'd like to be added
go.bsky.app/PY5tCas
go.bsky.app/FmERUoD
The first starter pack is full (they cap at 150), so I created a second one. Let me know if you'd like to be added
go.bsky.app/PY5tCas
go.bsky.app/FmERUoD
November 15, 2024 at 12:35 PM
Wonderful to see the #immunology community growing here.
The first starter pack is full (they cap at 150), so I created a second one. Let me know if you'd like to be added
go.bsky.app/PY5tCas
go.bsky.app/FmERUoD
The first starter pack is full (they cap at 150), so I created a second one. Let me know if you'd like to be added
go.bsky.app/PY5tCas
go.bsky.app/FmERUoD